some new tests, and reconfiguring

.github/CONTRIBUTING.md

@@ -22,7 +22,7 @@ New unit test suggestions are tracked as GitHub issues. When creating a unit tes
 4. Ensure your proposed WDL runs locally via `miniwdl run` or `java -jar cromwell-86.jar run`
 5. If you are user of PROOF, please also make sure to test that the WDL unit test runs via PROOF.
     - If your WDL succeeds locally but fails in PROOF, please report the issue in the [proof-api repo](https://github.com/FredHutch/proof-api/issues).
-6. Add the WDL to a subdirectory by the same name, i.e. `coolUnitTest/coolUnitTest.wdl`
+6. Add the WDL to a subdirectory by the same name, i.e. `coolUnitTest/coolUnitTest.wdl`. If the WDL is expected to fail WOMtool the subdirectory AND the WDL file name must start with `badVal`. If the WDL is expected to fail both WOMtool and a Cromwell run, then the subdirectory AND the WDL file name must start with `badRun`.
 7. Make sure to include an `inputs.json` and `options.json` if required and make sure that any other. input files referenced in `inputs.json` are provided in the same directory.
 8. Add a README to the WDL's subdirectory describing the unit test's functionality and purpose.
 9. Commit and push your proposed changes to GitHub.

.github/workflows/api-tests.yml

@@ -27,4 +27,4 @@ jobs:
       - name: Run tests
         env:
           PROOF_API_TOKEN_DEV: ${{ secrets.PROOF_API_TOKEN_DEV }}
-        run: uv run pytest tests/cromwell-api/ --verbose
+        run: uv run pytest tests/cromwellapi/ --verbose

badRunParseBatchFile/README.md

@@ -0,0 +1,15 @@
+# parseBatchFile WDL Workflow
+
+## Overview
+xxx
+
+## Workflow Components
+
+### Workflow: `parseBatchFile`
+xxx
+
+## Purpose
+To check Cromwell failures behavior
+
+## Version
+WDL 1.0

badRunParseBatchFile/badRunParseBatchFile.wdl

@@ -0,0 +1,46 @@
+version 1.0
+# This workflow takes a tab separated file where each row is a set of data to be used in each 
+# of the independent scattered task series that you have as your workflow process.  This file 
+# will, for example, have column names `sampleName`, `bamLocation`, and `bedlocation`.  This
+# allows you to know that regardless of the order of the columns in your batch file, the correct
+# inputs will be used for the tasks you define.  
+workflow parseBatchFile {
+  input {
+  File batchFile
+  }
+    Array[Object] batchInfo = read_objects(batchFile)
+  scatter (job in batchInfo){
+    String sampleName = job.sampleName
+    File bamFile = job.bamLocation
+    File bedFile = job.bedLocation
+
+    ## INSERT YOUR WORKFLOW TO RUN PER LINE IN YOUR BATCH FILE HERE!!!!
+    call test {
+        input: in1=sampleName, in2=bamFile, in3=bedFile
+    }
+
+  }  # End Scatter over the batch file
+# Outputs that will be retained when execution is complete
+  output {
+    Array[File] outputArray = test.item_out
+    }
+# End workflow
+}
+
+#### TASK DEFINITIONS
+# echo some text to stdout, treats files as strings just to echo them as a dummy example
+task test {
+  input {
+    String in1
+    String in2
+    String in3
+  }
+    command {
+    echo ~{in1}
+    echo ~{in2}
+    echo ~{in3}
+    }
+    output {
+        File item_out = stdout()
+    }
+}

badValMissingValue/README.md

@@ -0,0 +1,10 @@
+# badValMissingValue WDL Workflow
+
+## Overview
+A test workflow that demonstrates an invalid WDL.
+
+### Expected error
+
+```
+Cannot lookup value 'docker_image', it is never declared. Available values are: ['str']
+```

tests/cromwell-api/conftest.py → tests/cromwellapi/conftest.py

@@ -1,6 +1,7 @@
 from pathlib import Path
 
 import pytest
+
 from cromwell import CromwellApi
 from proof import ProofApi
 
@@ -13,7 +14,7 @@ def cromwell_api():
     return CromwellApi(url=cromwell_url)
 
 
-@pytest.fixture(scope="session", autouse=True)
+@pytest.fixture(scope="session")
 def submit_wdls(cromwell_api):
     """
     This fixture runs automatically before any tests.
@@ -25,7 +26,12 @@ def submit_wdls(cromwell_api):
 
     print(f"Submitting {len(wdl_paths)} wdls ...")
 
-    out = [cromwell_api.submit_workflow(wdl_path=path) for path in wdl_paths]
+    out = []
+    for path in wdl_paths:
+        opts_path = path.parent / "options.json"
+        opts_path = opts_path if opts_path.exists() else None
+        res = cromwell_api.submit_workflow(wdl_path=path, options=opts_path)
+        out.append(res)
 
     # Yield to let tests run
     yield out

tests/cromwellapi/cromwell.py

@@ -0,0 +1,144 @@
+import httpx
+from tenacity import (
+    retry,
+    retry_if_exception_type,
+    stop_after_attempt,
+    wait_exponential,
+)
+
+from utils import TOKEN, past_date
+
+
+def as_file_object(path=None):
+    if not path:
+        return None
+    return open(path, mode="rb")
+
+
+def my_before_sleep(state):
+    print(
+        f"Retrying in {state.next_action.sleep} seconds, attempt {state.attempt_number}"
+    )
+
+
+def path_as_string(x):
+    if not x:
+        return None
+    return str(x.absolute())
+
+
+class CromwellApi(object):
+    """CromwellApi class"""
+
+    def __init__(self, url):
+        self.base_url = url.rstrip("/")
+        self.token = TOKEN
+        self.headers = {"Authorization": f"Bearer {TOKEN}"}
+
+    def submit_workflow(
+        self,
+        wdl_path,
+        inputs=None,
+        labels=None,
+        options=None,
+    ):
+        files = {
+            "workflowSource": as_file_object(path_as_string(wdl_path)),
+            "workflowInputs": as_file_object(path_as_string(inputs)),
+            "labels": as_file_object(path_as_string(labels)),
+            "workflowOptions": as_file_object(path_as_string(options)),
+        }
+        files = {k: v for k, v in files.items() if v}
+        res = httpx.post(
+            f"{self.base_url}/api/workflows/v1", headers=self.headers, files=files
+        )
+        res.raise_for_status()
+        data = res.json()
+        data["path"] = str(wdl_path)
+        return data
+
+    @retry(
+        retry=retry_if_exception_type(httpx.HTTPStatusError),
+        stop=stop_after_attempt(3),
+        wait=wait_exponential(multiplier=1, min=4, max=10),
+        before_sleep=my_before_sleep,
+    )
+    def metadata(self, workflow_id, params={}):
+        res = httpx.get(
+            f"{self.base_url}/api/workflows/v1/{workflow_id}/metadata",
+            headers=self.headers,
+            params=params,
+        )
+        res.raise_for_status()
+        return res.json()
+
+    def version(self):
+        res = httpx.get(
+            f"{self.base_url}/engine/v1/version",
+            headers=self.headers,
+        )
+        res.raise_for_status()
+        return res.json()
+
+    def validate(self, wdl_path, inputs=None, options=None):
+        files = {
+            "workflowSource": as_file_object(path_as_string(wdl_path)),
+            "workflowInputs": as_file_object(path_as_string(inputs)),
+            "workflowOptions": as_file_object(path_as_string(options)),
+        }
+        files = {k: v for k, v in files.items() if v}
+        res = httpx.post(
+            f"{self.base_url}/api/womtool/v1/describe",
+            headers=self.headers,
+            files=files,
+        )
+        res.raise_for_status()
+        return res.json()
+
+    def abort(self, workflow_id):
+        res = httpx.post(
+            f"{self.base_url}/api/workflows/v1/{workflow_id}/abort",
+            headers=self.headers,
+        )
+        res.raise_for_status()
+        return res.json()
+
+    def search(self, days=1, name=None, status=None):
+        submission = f"{past_date(days)}T00:00Z"
+        params = {"submission": submission, "name": name, "status": status}
+        params = {k: v for k, v in params.items() if v}
+        res = httpx.get(
+            f"{self.base_url}/api/workflows/v1/query",
+            headers=self.headers,
+            params=params,
+        )
+        res.raise_for_status()
+        return res.json()
+
+    @retry(
+        retry=retry_if_exception_type(httpx.HTTPStatusError),
+        stop=stop_after_attempt(3),
+        wait=wait_exponential(multiplier=1, min=4, max=10),
+        before_sleep=my_before_sleep,
+    )
+    def outputs(self, workflow_id):
+        res = httpx.get(
+            f"{self.base_url}/api/workflows/v1/{workflow_id}/outputs",
+            headers=self.headers,
+        )
+        res.raise_for_status()
+        return res.json()
+
+    @retry(
+        retry=retry_if_exception_type(httpx.HTTPStatusError),
+        stop=stop_after_attempt(3),
+        wait=wait_exponential(multiplier=1, min=4, max=10),
+        before_sleep=my_before_sleep,
+    )
+    def labels(self, workflow_id):
+        res = httpx.get(
+            f"{self.base_url}/api/workflows/v1/{workflow_id}/labels",
+            headers=self.headers,
+        )
+        res.raise_for_status()
+        return res.json()

tests/cromwellapi/labels1.json

@@ -0,0 +1 @@
+{"workflowType": "AppSubmission", "Label": "one", "secondaryLabel": "two"}

tests/cromwell-api/proof.py → tests/cromwellapi/proof.py

@@ -1,4 +1,5 @@
 import httpx
+
 from utils import PROOF_BASE_URL, TOKEN